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"It is a lesson learned from last year," Fabrice Leggeri, the agency's chief, said at a ceremony on Thursday at a checkpoint on the Bulgaria and Turkey border.

But reports of the deaths and injuries of refugees aboard boats steered by smugglers under Frontex-led operations are raising tricky questions.

On 23 September, EU ombudsman Emily O'Reilly and Nils Muiznieks from the human rights watchdog Council of Europe were cc'd in a letter to Frontex that demanded answers over the shooting incidents.

The letter, signed by 42 MEPs, asks if the new agency will continue to use firearms against boats carrying refugees.

"Who takes the decision and/or the responsibility on the Frontex ships to shoot boats carrying refugees: the ship captain, Frontex headquarters on land, or member states’ coastal guards on land," it says.

Frontex in late August said a 17-year old was killed after the skipper of the yacht attacked Greek officers who had boarded the vessel following The Intercept report.

Leggeri, in a response to the MEP letter on 29 September, said that in half of the incidents reported, weapons were shot in the air with no possible harm to anyone.

In the remaining cases, he noted that shots were fired "upon attempts by the facilitators [smugglers] to violently ram the patrol vessel, putting in danger the lives of migrants and of the persons on board the patrolling vessel".

Frontex reloaded

Spooked by the some 1 million people that crossed through the Western Balkans to reach EU states, legislators rushed to transform Frontex into a more autonomous agency capable of deploying 1,500 border guards at a moment's notice.

The pool of guards will be made available before the end of the year.

The agency will oversee border control, sea rescue operations and the kicking out of rejected asylum seekers. But it will also offer operational support to countries outside the EU and share intelligence on cross-border criminal investigations.

"It also has a key role at Europe’s maritime borders through its new coast guard functions," said Leggeri in a press statement.

More money, more equipment

Warsaw-based Frontex has seen its budget and staffing numbers increase dramatically over the past few years.

The agency's budget was hiked by more than 75 percent this year to around €250 million, when compared with last year. It had already been increased three times in 2015.

Under its new mandate, the agency will be able to lease its own equipment instead of having to exclusively rely on member states.

Its powers also extend to telling EU states how to best secure their outside borders, a touchy area for national authorities, at the risk of imposing internal border controls for up to six months should they fail to comply.

Five EU states have so far volunteered to undergo the agency's stress tests to assess possible external border gaps. Initial results are expect early next year.

This article was updated on 6 October at 15:00 to include Leggeri's response to the MEPs

Leaders at the EU summit are unlikely to discuss migration, preferring instead to rubber-stamp pre-cooked conclusions. Recent proposals by the European Commission to get some of the reforms finalised are also unlikely to get broad support. The two-year deadlock continues.

EUobserved

The European Commission claims sea crossings from Libya are more dangerous because smugglers are using less seaworthy boats. But it fails to explain why that is - an omission of their own policies of boat capture and seizure.

The European Commission wants EU states to voluntarily accept rescued asylum seekers - in a plan that would then phase out when the stalled reforms on the 'Dublin' regulation, which imposes relocation, are sorted.